to do - Githubissues

MrTomRod / scoary-2

Calculate assocations between genes and traits

MIT License

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to do #1

Open MrTomRod opened 2 years ago

MrTomRod commented 2 years ago

[x] add metadata to dendrogram
[x] cpd search feature
[x] add dendrogram to trait view -> allow recoloring
[ ] in dendrogram: instead of only gene presence-absence, show gene count!
[x] does Roary gene_presence_absence.csv include gene identifiers? (yes)

jacordova commented 2 years ago

Hello Tom, out of curiosity is Scoary2 ready to run? Thank you.

MrTomRod commented 2 years ago

Hey!

Yes, it should work, but you'd be the first person to try it out. Give me another 20 minutes to push the latest changes into version 0.0.6. Can you give a description of what your datasets look like?

n orthogenes
n isolates
n traits
are the traits numeric?
which software did you use to create the orthogene dataset?

MrTomRod commented 2 years ago

Done!

Don't hesitate to ask me if something is not clear and please report any bugs you might encounter.

jacordova commented 2 years ago

Hi Tom,

Thanks!

Sure, here's that info:

n orthogenes = either 27,778 (from Roary) or 14,849 (from OrthoMCL); I'm looking into why one has more than the other.
n isolates = 182
n traits = 2 (growth in aerobic and growth in anaerobic)
Yes, the traits are numeric
I ran both Roary and OrthoMCL, though I'm trying to look into why one produces more orthogenes than the other

MrTomRod commented 2 years ago

And how may different species?

Consider also testing OrthoFinder, my favourite ortholog tool and maybe currently the best one.

jacordova commented 2 years ago

I'm working with two species but I'm doing them individually, then together.